Religion and politics are major threads in the fabric of our society and therefore, are open for discussion. The discussion, in an ideal world, would lead to a greater understand of different religions and opposing political views and would result in less animosity and better understanding. Unfortunately, we do not live in an ideal world and some people raise the subjects just to start arguments and others will raise the issues because they believe they have an important point to make or wish to create a misunderstanding.
Since there are no real rules on the internet, the discussion of either can turn very hostile. Other subjects like gun control, the economy and education can create equally heated discussions.
The best way to handle it is to voice your view, if you have something to offer, as politely and professionally as possible. You do not have to respond to all comments or replies. You can voice your viewpoint and end the discussion. The one thing that everyone needs to learn to do is not to let the discussion get hijacked by a person who just likes to argue. On Hub Pages, there are a group of Hubbers, who have never written a hub--a concept that is hard to understand, but they like to get to involve in the discussions. I have learned to either end of debate, ignore the comment or delete the comment if it has no bearing on the discussion. Many that I disagree with remain, as long as they are not presented in a rude or derogatory manner.